03-01-2020
This forum is not a script writing service.
If you have a solution you have worked on that is not complete we can help you, but you must have shown some effort to solve this yourself.
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hi,
I am new to this forum and new to awk.
I have a file that contains 2 columns.
Heres an example of what it looks like:
10 +
20 +
40 +
50 -
70 -
So the file is tab-delimited. What I want to do is add 10 to column 1 whenever column 2 is + and substract 10 from column 1... (1 Reply)
Discussion started by: phil_heath
1 Replies
2. Shell Programming and Scripting
Dear All,
I would like to split a file of the following format into multiple files based on the number in the 6th column (numbers 1, 2, 3...):
ATOM 1 N GLY A 1 -3.198 27.537 -5.958 1.00 0.00 N
ATOM 2 CA GLY A 1 -2.199 28.399 -6.617 1.00 0.00 ... (3 Replies)
Discussion started by: tomasl
3 Replies
3. Shell Programming and Scripting
Hi,
I have a file sample_1.txt (300k rows) which has data like below:
* Also each record is around 64k bytes
11|1|abc|102553|125589|64k bytes of data
10|2|def|123452|123356|......
13|2|geh|144351|121123|...
25|4|fgh|165250|118890|..
14|1|abc|186149|116657|......... (6 Replies)
Discussion started by: sol_nov
6 Replies
4. Shell Programming and Scripting
I have a following inputfile
MT,AP,CDM,TTML,MUM,GS,SUCC,3
MT,AP,CDM,TTSL,AP,GS,FAIL,9
MT,AP,CDM,RCom,MAH,GS,SUCC,3
MT,AP,CDM,RTL,HP,GS,SUCC,1
MT,AP,CDM,Uni,UPE,GS,SUCC,2
MT,AP,CDM,Uni,MUM,GS,SUCC,2
TTSL,AP,GS,MT,MAH,CDM,SUCC,20
TTML,AP,GS,MT,MAH,CDM,FAIL,10... (2 Replies)
Discussion started by: siramitsharma
2 Replies
5. Shell Programming and Scripting
Hi,
I have a similar input format-
A_1 2
B_0 4
A_1 1
B_2 5
A_4 1
and looking to print in this output format with headers. can you suggest in awk?awk because i am doing some pattern matching from parent file to print column 1 of my input using awk already.Thanks!
letter number_of_letters... (5 Replies)
Discussion started by: prashob123
5 Replies
6. Shell Programming and Scripting
Hi,
I have a table to be imported for R as matrix or data.frame but I first need to edit it because I've got several lines with the same identifier (1st column), so I want to sum the each column (2nd -nth) of each identifier (1st column)
The input is for example, after sorted:
K00001 1 1 4 3... (8 Replies)
Discussion started by: sargotrons
8 Replies
7. Shell Programming and Scripting
please write a shell script
Table
--------------------------
1 2 3 a b c
3 4 5 c d e
7 8 9 f g h
Output should be like this
---------------
1 2 3
3 4 5
7 8 9
a b c
c d e
f g h (1 Reply)
Discussion started by: Priti2277
1 Replies
8. Shell Programming and Scripting
Split column data if the table has n number of column's with some record then how to split n number of colmn's line by line with records
Table
---------
Col1 col2 col3 col4 ....................col20
1 2 3 4 .................... 20
a b c d .................... v
... (11 Replies)
Discussion started by: Priti2277
11 Replies
9. Shell Programming and Scripting
Hello,
I am trying to store sum of a column as a new column inside a file but have to find the column names dynamically
I/p
c1,c2,c3,c4,c5
10,20,30,40,50
20,30,40,50,60
If i want to find sum only column c1, c3 and output it as c6,c7
O/p
c1,c2,c3,c4,c5,c6,c7
10,20,30,40,50,30,70... (6 Replies)
Discussion started by: mkathi
6 Replies
10. UNIX for Beginners Questions & Answers
Hi All,
I have a file as below and want to sum based on the id in the first column
Input
10264;ATE; 12
10265;SES;11
10266AUT;50
10264;ATE;10
10265;SES;13
10266AUT;89
10264;ATE;1
10265;SES;15
10266AUT;78
Output
10264;ATE; 23
10265;SES;39
10266AUT;139 (6 Replies)
Discussion started by: arunkumar_mca
6 Replies
LEARN ABOUT DEBIAN
bio::featureio::bed
Bio::FeatureIO::bed(3pm) User Contributed Perl Documentation Bio::FeatureIO::bed(3pm)
NAME
Bio::FeatureIO::bed - read/write features from UCSC BED format
SYNOPSIS
my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
for my $feat ($in->next_feature) {
# do something with $feat (a Bio::SeqFeature::Annotated object)
}
my $out = Bio::FeatureIO(-format=>'bed');
for my $feat ($seq->get_seqFeatures) {
$out->write_feature($feat);
}
DESCRIPTION
See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.
Currently for read and write only the first 6 fields (chr, start, end, name, score, strand) are supported.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Allen Day
Email allenday@ucla.edu
CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_initialize
Title : _initialize
Function: initializes BED for reading/writing
Args : all optional:
name description
----------------------------------------------------------
-name the name for the BED track, stored in header
name defaults to localtime()
-description the description for the BED track, stored in
header. defaults to localtime().
-use_score whether or not the score attribute of
features should be used when rendering them.
the higher the score the darker the color.
defaults to 0 (false)
use_score
Title : use_score
Usage : $obj->use_score($newval)
Function: should score be used to adjust feature color when rendering? set to true if so.
Example :
Returns : value of use_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
name
Title : name
Usage : $obj->name($newval)
Function: name of BED track
Example :
Returns : value of name (a scalar)
Args : on set, new value (a scalar or undef, optional)
description
Title : description
Usage : $obj->description($newval)
Function: description of BED track
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::FeatureIO::bed(3pm)